The EcoCyc Database in 2021

Ingrid M. Keseler, Socorro Gama-Castro, Amanda Mackie, Richard Billington, César Bonavides-Martínez, Ron Caspi, Anamika Kothari, Markus Krummenacker, Peter E. Midford, Luis Muñiz-Rascado, Wai Kit Ong, Suzanne Paley, Alberto Santos-Zavaleta, Pallavi Subhraveti, Víctor H. Tierrafría, Alan J. Wolfe, Julio Collado-Vides, Ian T. Paulsen, Peter D. Karp*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    25 Citations (Scopus)
    21 Downloads (Pure)

    Abstract

    The EcoCyc model-organism database collects and summarizes experimental data for Escherichia coli K-12. EcoCyc is regularly updated by the manual curation of individual database entries, such as genes, proteins, and metabolic pathways, and by the programmatic addition of results from select high-throughput analyses. Updates to the Pathway Tools software that supports EcoCyc and to the web interface that enables user access have continuously improved its usability and expanded its functionality. This article highlights recent improvements to the curated data in the areas of metabolism, transport, DNA repair, and regulation of gene expression. New and revised data analysis and visualization tools include an interactive metabolic network explorer, a circular genome viewer, and various improvements to the speed and usability of existing tools.

    Original languageEnglish
    Article number711077
    Pages (from-to)1-10
    Number of pages10
    JournalFrontiers in Microbiology
    Volume12
    DOIs
    Publication statusPublished - Jul 2021

    Bibliographical note

    Copyright the Author(s) 2021. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

    Keywords

    • Escherichia coli
    • EcoCyc
    • drug efflux transporters
    • metabolism
    • model-organism database
    • gene regulation

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